Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-151_S2_L002_R1_001_val_1.fq.gz to EPI-151_S2_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-151_S2_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-151_S2_L002_R2_001_val_2.fq.gz to EPI-151_S2_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-151_S2_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-151_S2_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-151_S2_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-151_S2_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-151_S2_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1928:2248_1:N:0:ATCACG/1 77 * 0 0 * * 0 0 TAGTAGAGGTTTATATGTATTTATGTTTGGTTAGAAAAGGTTTATATGTATTTATGTTTGGTTAGTAGAGGTTTATATGTATTTATGTTTGGTTA BBBBBFFBFFBBFBBBBFFF/B/FBBF>> Writing bisulfite mapping results to EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99800 (99.80%) aligned concordantly 0 times 200 (0.20%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.20% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99579 (99.58%) aligned concordantly 0 times 421 (0.42%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.42% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-151_S2_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-151_S2_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 621 Mapping efficiency: 0.6% Sequence pairs with no alignments under any condition: 99379 Sequence pairs did not map uniquely: 0 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 421 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 200 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 24525 Total methylated C's in CpG context: 75 Total methylated C's in CHG context: 309 Total methylated C's in CHH context: 104 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 6962 Total unmethylated C's in CHG context: 6893 Total unmethylated C's in CHH context: 10182 Total unmethylated C's in Unknown context: 2 C methylated in CpG context: 1.1% C methylated in CHG context: 4.3% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 0.0% Bismark completed in 0d 0h 0m 11s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-152_S3_L002_R1_001_val_1.fq.gz to EPI-152_S3_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-152_S3_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-152_S3_L002_R2_001_val_2.fq.gz to EPI-152_S3_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-152_S3_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-152_S3_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-152_S3_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-152_S3_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-152_S3_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1155:2233_1:N:0:CGATGT/1 77 * 0 0 * * 0 0 AATGGNTATGAAAATGTAATAAAGGAAGAGATATGAAAATGTAATAAAGGAANATTTATGANAATGTATTGTGGGAAGTGATATGAAAATGTAATATG BBBBB#B>> Writing bisulfite mapping results to EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99688 (99.69%) aligned concordantly 0 times 312 (0.31%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.31% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99843 (99.84%) aligned concordantly 0 times 157 (0.16%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.16% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-152_S3_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-152_S3_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 469 Mapping efficiency: 0.5% Sequence pairs with no alignments under any condition: 99531 Sequence pairs did not map uniquely: 0 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 312 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 157 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 19248 Total methylated C's in CpG context: 48 Total methylated C's in CHG context: 198 Total methylated C's in CHH context: 87 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 5447 Total unmethylated C's in CHG context: 5293 Total unmethylated C's in CHH context: 8175 Total unmethylated C's in Unknown context: 1 C methylated in CpG context: 0.9% C methylated in CHG context: 3.6% C methylated in CHH context: 1.1% C methylated in unknown context (CN or CHN): 0.0% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-153_S4_L002_R1_001_val_1.fq.gz to EPI-153_S4_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-153_S4_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-153_S4_L002_R2_001_val_2.fq.gz to EPI-153_S4_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-153_S4_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-153_S4_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-153_S4_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-153_S4_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-153_S4_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1785:2231_1:N:0:TTAGGC/1 77 * 0 0 * * 0 0 TGTTGNGATATATAATTGAAAATTGTTGAAAGTGTTATTAAATATAATGTAATAATAAATGATAAAGGGATGTAATGTTGTATATTAATTATTAT BBBBB#BBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP D00743:144:CAAWNANXX:2:2207:1785:2231_2:N:0:TTAGGC/2 141 * 0 0 * * 0 0 ATANNNNNNNNNNNNNNNNNNNNNNNNNNNNTNNNATTTATTATTACATTATATTTAATAACACTTTCAACAATTTTCAATTATATATCACAACA BBB############################B###BB<>> Writing bisulfite mapping results to EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99568 (99.57%) aligned concordantly 0 times 432 (0.43%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.43% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99795 (99.80%) aligned concordantly 0 times 205 (0.20%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.20% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-153_S4_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-153_S4_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 637 Mapping efficiency: 0.6% Sequence pairs with no alignments under any condition: 99363 Sequence pairs did not map uniquely: 0 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 432 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 205 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 26175 Total methylated C's in CpG context: 100 Total methylated C's in CHG context: 289 Total methylated C's in CHH context: 159 Total methylated C's in Unknown context: 12 Total unmethylated C's in CpG context: 7435 Total unmethylated C's in CHG context: 7145 Total unmethylated C's in CHH context: 11047 Total unmethylated C's in Unknown context: 5 C methylated in CpG context: 1.3% C methylated in CHG context: 3.9% C methylated in CHH context: 1.4% C methylated in unknown context (CN or CHN): 70.6% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-154_S5_L002_R1_001_val_1.fq.gz to EPI-154_S5_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-154_S5_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-154_S5_L002_R2_001_val_2.fq.gz to EPI-154_S5_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-154_S5_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-154_S5_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-154_S5_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-154_S5_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-154_S5_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:2191:2242_1:N:0:TGACCA/1 77 * 0 0 * * 0 0 ATGTANATTAAGAGTTAAATTATGTAGATGTAGATTAAAAGTTAAATTATGTATAGGTAGATTAAGAGTTAAATTAAGTAGATGTAGATTAAGAGTTTAAT BBBBB#>> Writing bisulfite mapping results to EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99736 (99.74%) aligned concordantly 0 times 264 (0.26%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.26% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99435 (99.44%) aligned concordantly 0 times 565 (0.56%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.56% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-154_S5_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-154_S5_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 829 Mapping efficiency: 0.8% Sequence pairs with no alignments under any condition: 99171 Sequence pairs did not map uniquely: 0 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 565 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 264 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 33555 Total methylated C's in CpG context: 112 Total methylated C's in CHG context: 380 Total methylated C's in CHH context: 145 Total methylated C's in Unknown context: 5 Total unmethylated C's in CpG context: 9663 Total unmethylated C's in CHG context: 9316 Total unmethylated C's in CHH context: 13939 Total unmethylated C's in Unknown context: 15 C methylated in CpG context: 1.1% C methylated in CHG context: 3.9% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 25.0% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-159_S6_L002_R1_001_val_1.fq.gz to EPI-159_S6_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-159_S6_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-159_S6_L002_R2_001_val_2.fq.gz to EPI-159_S6_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-159_S6_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-159_S6_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-159_S6_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-159_S6_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-159_S6_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1469:2230_1:N:0:ACAGTG/1 77 * 0 0 * * 0 0 GGTTANTGAAGTGTATATAGTTATATTGTAAATTAATGGTTGAGTGAGTTTTNTTTTTTATTAGGTAATATTTTAAGGGAATGGTTGTTTGTAAATATTGG BBBBB#BBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFFFFFF#<>> Writing bisulfite mapping results to EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99862 (99.86%) aligned concordantly 0 times 138 (0.14%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.14% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99650 (99.65%) aligned concordantly 0 times 350 (0.35%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.35% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-159_S6_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-159_S6_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 488 Mapping efficiency: 0.5% Sequence pairs with no alignments under any condition: 99512 Sequence pairs did not map uniquely: 0 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 350 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 138 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 19125 Total methylated C's in CpG context: 72 Total methylated C's in CHG context: 192 Total methylated C's in CHH context: 85 Total methylated C's in Unknown context: 2 Total unmethylated C's in CpG context: 5542 Total unmethylated C's in CHG context: 5229 Total unmethylated C's in CHH context: 8005 Total unmethylated C's in Unknown context: 4 C methylated in CpG context: 1.3% C methylated in CHG context: 3.5% C methylated in CHH context: 1.1% C methylated in unknown context (CN or CHN): 33.3% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-160_S7_L002_R1_001_val_1.fq.gz to EPI-160_S7_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-160_S7_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-160_S7_L002_R2_001_val_2.fq.gz to EPI-160_S7_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-160_S7_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-160_S7_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-160_S7_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-160_S7_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-160_S7_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1522:2231_1:N:0:GCCAAT/1 77 * 0 0 * * 0 0 GTATGNGTAATTAGGTGATTTTTTTTGATTTGATGTAGTTAGTGGATTGGGAATTGGTAA BBBBB#BBBFFBFFFFFFFFFFFFFFB/>> Writing bisulfite mapping results to EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 98785 (98.78%) aligned concordantly 0 times 1215 (1.22%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 1.22% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99390 (99.39%) aligned concordantly 0 times 610 (0.61%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.61% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-160_S7_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-160_S7_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 1825 Mapping efficiency: 1.8% Sequence pairs with no alignments under any condition: 98175 Sequence pairs did not map uniquely: 0 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 1215 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 610 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 67790 Total methylated C's in CpG context: 214 Total methylated C's in CHG context: 788 Total methylated C's in CHH context: 347 Total methylated C's in Unknown context: 8 Total unmethylated C's in CpG context: 19193 Total unmethylated C's in CHG context: 18392 Total unmethylated C's in CHH context: 28856 Total unmethylated C's in Unknown context: 24 C methylated in CpG context: 1.1% C methylated in CHG context: 4.1% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 25.0% Bismark completed in 0d 0h 0m 11s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-161_S8_L002_R1_001_val_1.fq.gz to EPI-161_S8_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-161_S8_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-161_S8_L002_R2_001_val_2.fq.gz to EPI-161_S8_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-161_S8_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-161_S8_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-161_S8_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-161_S8_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-161_S8_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:2010:2229_1:N:0:CAGATC/1 77 * 0 0 * * 0 0 TGATANGTAGTATATGGTGTATGATATAGTA BBBBB#>> Writing bisulfite mapping results to EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99630 (99.63%) aligned concordantly 0 times 370 (0.37%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.37% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99783 (99.78%) aligned concordantly 0 times 217 (0.22%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.22% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-161_S8_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-161_S8_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 587 Mapping efficiency: 0.6% Sequence pairs with no alignments under any condition: 99413 Sequence pairs did not map uniquely: 0 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 370 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 217 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 22950 Total methylated C's in CpG context: 98 Total methylated C's in CHG context: 237 Total methylated C's in CHH context: 100 Total methylated C's in Unknown context: 5 Total unmethylated C's in CpG context: 6548 Total unmethylated C's in CHG context: 6286 Total unmethylated C's in CHH context: 9681 Total unmethylated C's in Unknown context: 4 C methylated in CpG context: 1.5% C methylated in CHG context: 3.6% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 55.6% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-162_S9_L002_R1_001_val_1.fq.gz to EPI-162_S9_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-162_S9_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-162_S9_L002_R2_001_val_2.fq.gz to EPI-162_S9_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-162_S9_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-162_S9_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-162_S9_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-162_S9_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-162_S9_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1238:2233_1:N:0:ACTTGA/1 77 * 0 0 * * 0 0 TGTTANTTATTTTAAAATTTGTTGATAAATTGTTTATTTTTAGGATAGTTTTTTTAGATATTGTTTTTTTTTGGTTTGAAAGGGTTATGAATAGTTTTTTT BBBBB#>> Writing bisulfite mapping results to EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99804 (99.80%) aligned concordantly 0 times 196 (0.20%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.20% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99581 (99.58%) aligned concordantly 0 times 419 (0.42%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.42% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-162_S9_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-162_S9_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 615 Mapping efficiency: 0.6% Sequence pairs with no alignments under any condition: 99385 Sequence pairs did not map uniquely: 0 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 419 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 196 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 22576 Total methylated C's in CpG context: 83 Total methylated C's in CHG context: 302 Total methylated C's in CHH context: 127 Total methylated C's in Unknown context: 4 Total unmethylated C's in CpG context: 6495 Total unmethylated C's in CHG context: 6133 Total unmethylated C's in CHH context: 9436 Total unmethylated C's in Unknown context: 6 C methylated in CpG context: 1.3% C methylated in CHG context: 4.7% C methylated in CHH context: 1.3% C methylated in unknown context (CN or CHN): 40.0% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-167_S10_L002_R1_001_val_1.fq.gz to EPI-167_S10_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-167_S10_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-167_S10_L002_R2_001_val_2.fq.gz to EPI-167_S10_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-167_S10_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-167_S10_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-167_S10_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-167_S10_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-167_S10_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1666:2232_1:N:0:GATCAG/1 77 * 0 0 * * 0 0 TTGAANTTGTTGATTTATATGGGGATATGAATAATAAGTTTAATATTTAAGATGGAGAAGAAATAAGTGTAGAATTTTGGATAAAGGATAATTAAGTTAAT BBBBB#BBFFFFFF>> Writing bisulfite mapping results to EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99503 (99.50%) aligned concordantly 0 times 497 (0.50%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.50% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99716 (99.72%) aligned concordantly 0 times 284 (0.28%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.28% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-167_S10_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-167_S10_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 781 Mapping efficiency: 0.8% Sequence pairs with no alignments under any condition: 99219 Sequence pairs did not map uniquely: 0 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 497 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 284 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 36053 Total methylated C's in CpG context: 189 Total methylated C's in CHG context: 367 Total methylated C's in CHH context: 300 Total methylated C's in Unknown context: 5 Total unmethylated C's in CpG context: 10550 Total unmethylated C's in CHG context: 10313 Total unmethylated C's in CHH context: 14334 Total unmethylated C's in Unknown context: 13 C methylated in CpG context: 1.8% C methylated in CHG context: 3.4% C methylated in CHH context: 2.1% C methylated in unknown context (CN or CHN): 27.8% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-168_S11_L002_R1_001_val_1.fq.gz to EPI-168_S11_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-168_S11_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-168_S11_L002_R2_001_val_2.fq.gz to EPI-168_S11_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-168_S11_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-168_S11_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-168_S11_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-168_S11_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-168_S11_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1424:2239_1:N:0:TAGCTT/1 77 * 0 0 * * 0 0 GTGATNTATAATGTATTATTGAAAGTTAATAGTTTATTTAAGTTTTTGGTATTTTTTGATTTAGGTTTAATTATTTTGTTATGTGGGTTTGTGATTTG BBBBB#B>> Writing bisulfite mapping results to EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99818 (99.82%) aligned concordantly 0 times 182 (0.18%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.18% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99603 (99.60%) aligned concordantly 0 times 397 (0.40%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.40% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-168_S11_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-168_S11_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 579 Mapping efficiency: 0.6% Sequence pairs with no alignments under any condition: 99421 Sequence pairs did not map uniquely: 0 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 397 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 182 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 23642 Total methylated C's in CpG context: 71 Total methylated C's in CHG context: 251 Total methylated C's in CHH context: 126 Total methylated C's in Unknown context: 2 Total unmethylated C's in CpG context: 6804 Total unmethylated C's in CHG context: 6632 Total unmethylated C's in CHH context: 9758 Total unmethylated C's in Unknown context: 7 C methylated in CpG context: 1.0% C methylated in CHG context: 3.6% C methylated in CHH context: 1.3% C methylated in unknown context (CN or CHN): 22.2% Bismark completed in 0d 0h 0m 11s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-169_S12_L002_R1_001_val_1.fq.gz to EPI-169_S12_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-169_S12_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-169_S12_L002_R2_001_val_2.fq.gz to EPI-169_S12_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-169_S12_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-169_S12_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-169_S12_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-169_S12_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-169_S12_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:1452:2231_1:N:0:GGCTAC/1 77 * 0 0 * * 0 0 TGGTANGAGGTTGTGTGATTAGTATAAAGGTGTTTAGAGTTATTAAGTGGATTGGATTGGAGTTTGGATTGGTTTTGTATTAATAAAAGTGTTTTTTTTGT BBBBB#<>> Writing bisulfite mapping results to EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99780100000 ( reads; of these:99.78 % ) aligned concordantly 0 times100000 ( 220 (0.22%) aligned concordantly exactly 1 time100.00 % ) were paired; of these:0 ( 0.0099898% () aligned concordantly >1 times99.90 %0.22) aligned concordantly 0 times% overall alignment rate 102 (0.10%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.10% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-169_S12_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-169_S12_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 322 Mapping efficiency: 0.3% Sequence pairs with no alignments under any condition: 99678 Sequence pairs did not map uniquely: 0 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 220 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 102 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 12209 Total methylated C's in CpG context: 55 Total methylated C's in CHG context: 153 Total methylated C's in CHH context: 62 Total methylated C's in Unknown context: 2 Total unmethylated C's in CpG context: 3518 Total unmethylated C's in CHG context: 3274 Total unmethylated C's in CHH context: 5147 Total unmethylated C's in Unknown context: 0 C methylated in CpG context: 1.5% C methylated in CHG context: 4.5% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 100.0% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/lambda/ (absolute path is '/gscratch/srlab/sr320/data/lambda/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/1104'): /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R2_001_val_2.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/1104 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/lambda/ chr J02459.1 (48502 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R2_001_val_2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz Writing a C -> T converted version of the input file EPI-170_S13_L002_R1_001_val_1.fq.gz to EPI-170_S13_L002_R1_001_val_1.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file EPI-170_S13_L002_R1_001_val_1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R2_001_val_2.fq.gz Writing a G -> A converted version of the input file EPI-170_S13_L002_R2_001_val_2.fq.gz to EPI-170_S13_L002_R2_001_val_2.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file EPI-170_S13_L002_R2_001_val_2.fq.gz (100001 sequences in total) Input files are EPI-170_S13_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-170_S13_L002_R2_001_val_2.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from EPI-170_S13_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-170_S13_L002_R2_001_val_2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: D00743:144:CAAWNANXX:2:2207:2244:2228_1:N:0:CTTGTA/1 77 * 0 0 * * 0 0 TTGTTNAGTTTGTTTAAGTTATTTTGATTTGTTAAAAAATATGGTAG BBBBB#<>> Writing bisulfite mapping results to EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R2_001_val_2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99849 (99.85%) aligned concordantly 0 times 151 (0.15%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.15% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99687 (99.69%) aligned concordantly 0 times 313 (0.31%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 0.31% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files EPI-170_S13_L002_R1_001_val_1.fq.gz_C_to_T.fastq and EPI-170_S13_L002_R2_001_val_2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 464 Mapping efficiency: 0.5% Sequence pairs with no alignments under any condition: 99536 Sequence pairs did not map uniquely: 0 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 313 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 151 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 16764 Total methylated C's in CpG context: 51 Total methylated C's in CHG context: 230 Total methylated C's in CHH context: 80 Total methylated C's in Unknown context: 2 Total unmethylated C's in CpG context: 4862 Total unmethylated C's in CHG context: 4524 Total unmethylated C's in CHH context: 7017 Total unmethylated C's in Unknown context: 4 C methylated in CpG context: 1.0% C methylated in CHG context: 4.8% C methylated in CHH context: 1.1% C methylated in unknown context (CN or CHN): 33.3% Bismark completed in 0d 0h 0m 10s ==================== Bismark run complete ==================== Processing paired-end Bismark output file(s) (SAM format): EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam: 621 Total number duplicated alignments removed: 67 (10.79%) Duplicated alignments were found at: 42 different position(s) Total count of deduplicated leftover sequences: 554 (89.21% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam: 469 Total number duplicated alignments removed: 40 (8.53%) Duplicated alignments were found at: 31 different position(s) Total count of deduplicated leftover sequences: 429 (91.47% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam: 637 Total number duplicated alignments removed: 28 (4.40%) Duplicated alignments were found at: 21 different position(s) Total count of deduplicated leftover sequences: 609 (95.60% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam: 829 Total number duplicated alignments removed: 95 (11.46%) Duplicated alignments were found at: 55 different position(s) Total count of deduplicated leftover sequences: 734 (88.54% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam: 488 Total number duplicated alignments removed: 36 (7.38%) Duplicated alignments were found at: 29 different position(s) Total count of deduplicated leftover sequences: 452 (92.62% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam: 1825 Total number duplicated alignments removed: 285 (15.62%) Duplicated alignments were found at: 159 different position(s) Total count of deduplicated leftover sequences: 1540 (84.38% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam: 587 Total number duplicated alignments removed: 54 (9.20%) Duplicated alignments were found at: 38 different position(s) Total count of deduplicated leftover sequences: 533 (90.80% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam: 615 Total number duplicated alignments removed: 38 (6.18%) Duplicated alignments were found at: 31 different position(s) Total count of deduplicated leftover sequences: 577 (93.82% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam: 781 Total number duplicated alignments removed: 3 (0.38%) Duplicated alignments were found at: 3 different position(s) Total count of deduplicated leftover sequences: 778 (99.62% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam: 579 Total number duplicated alignments removed: 34 (5.87%) Duplicated alignments were found at: 27 different position(s) Total count of deduplicated leftover sequences: 545 (94.13% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam: 322 Total number duplicated alignments removed: 16 (4.97%) Duplicated alignments were found at: 12 different position(s) Total count of deduplicated leftover sequences: 306 (95.03% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R2_001_val_2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam: 464 Total number duplicated alignments removed: 18 (3.88%) Duplicated alignments were found at: 15 different position(s) Total count of deduplicated leftover sequences: 446 (96.12% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:J02459.1 LN:48502 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R2_001_val_2.fq.gz" *** Bismark methylation extractor version v0.21.0 *** Trying to determine the type of mapping from the SAM header line of file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Treating file(s) as paired-end data (as extracted from @PG line) Setting option '--no_overlap' since this is (normally) the right thing to do for paired-end data Summarising Bismark methylation extractor parameters: =============================================================== Bismark paired-end SAM format specified (default) Number of cores to be used: 14 Output will be written to the current directory ('/gscratch/scrubbed/sr320/1104') Summarising bedGraph parameters: =============================================================== Generating additional output in bedGraph and coverage format bedGraph format: coverage format: Using a cutoff of 1 read(s) to report cytosine positions Reporting and sorting cytosine methylation information in CpG context only (default) The bedGraph UNIX sort command will use the following memory setting: '75%'. Temporary directory used for sorting is the output directory Checking file >>EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R2_001_val_2.fq.gz" Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 554 lines in total Total number of methylation call strings processed: 1108 Final Cytosine Methylation Report ================================= Total number of C's analysed: 14731 Total methylated C's in CpG context: 52 Total methylated C's in CHG context: 173 Total methylated C's in CHH context: 63 Total C to T conversions in CpG context: 4112 Total C to T conversions in CHG context: 4085 Total C to T conversions in CHH context: 6246 C methylated in CpG context: 1.2% C methylated in CHG context: 4.1% C methylated in CHH context: 1.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104/CpG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104/CpG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 429 lines in total Total number of methylation call strings processed: 858 Final Cytosine Methylation Report ================================= Total number of C's analysed: 11618 Total methylated C's in CpG context: 33 Total methylated C's in CHG context: 119 Total methylated C's in CHH context: 55 Total C to T conversions in CpG context: 3293 Total C to T conversions in CHG context: 3160 Total C to T conversions in CHH context: 4958 C methylated in CpG context: 1.0% C methylated in CHG context: 3.6% C methylated in CHH context: 1.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104/CpG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104/CpG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R2_001_val_2.fq.gz" Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 609 lines in total Total number of methylation call strings processed: 1218 Final Cytosine Methylation Report ================================= Total number of C's analysed: 16860 Total methylated C's in CpG context: 63 Total methylated C's in CHG context: 182 Total methylated C's in CHH context: 108 Total C to T conversions in CpG context: 4751 Total C to T conversions in CHG context: 4561 Total C to T conversions in CHH context: 7195 C methylated in CpG context: 1.3% C methylated in CHG context: 3.8% C methylated in CHH context: 1.5% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104/CpG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104/CpG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 734 lines in total Total number of methylation call strings processed: 1468 Final Cytosine Methylation Report ================================= Total number of C's analysed: 19966 Total methylated C's in CpG context: 72 Total methylated C's in CHG context: 222 Total methylated C's in CHH context: 91 Total C to T conversions in CpG context: 5701 Total C to T conversions in CHG context: 5462 Total C to T conversions in CHH context: 8418 C methylated in CpG context: 1.2% C methylated in CHG context: 3.9% C methylated in CHH context: 1.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104/CpG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104/CpG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-159_S6_L002_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 452 lines in total Total number of methylation call strings processed: 904 Final Cytosine Methylation Report ================================= Total number of C's analysed: 12096 Total methylated C's in CpG context: 42 Total methylated C's in CHG context: 122 Total methylated C's in CHH context: 55 Total C to T conversions in CpG context: 3449 Total C to T conversions in CHG context: 3269 Total C to T conversions in CHH context: 5159 C methylated in CpG context: 1.2% C methylated in CHG context: 3.6% C methylated in CHH context: 1.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104/CpG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104/CpG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-160_S7_L002_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 1540 lines in total Total number of methylation call strings processed: 3080 Final Cytosine Methylation Report ================================= Total number of C's analysed: 37041 Total methylated C's in CpG context: 119 Total methylated C's in CHG context: 404 Total methylated C's in CHH context: 194 Total C to T conversions in CpG context: 10386 Total C to T conversions in CHG context: 9934 Total C to T conversions in CHH context: 16004 C methylated in CpG context: 1.1% C methylated in CHG context: 3.9% C methylated in CHH context: 1.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104/CpG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104/CpG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-161_S8_L002_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 533 lines in total Total number of methylation call strings processed: 1066 Final Cytosine Methylation Report ================================= Total number of C's analysed: 13454 Total methylated C's in CpG context: 56 Total methylated C's in CHG context: 130 Total methylated C's in CHH context: 61 Total C to T conversions in CpG context: 3815 Total C to T conversions in CHG context: 3620 Total C to T conversions in CHH context: 5772 C methylated in CpG context: 1.4% C methylated in CHG context: 3.5% C methylated in CHH context: 1.0% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104/CpG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104/CpG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 577 lines in total Total number of methylation call strings processed: 1154 Final Cytosine Methylation Report ================================= Total number of C's analysed: 13600 Total methylated C's in CpG context: 46 Total methylated C's in CHG context: 163 Total methylated C's in CHH context: 77 Total C to T conversions in CpG context: 3867 Total C to T conversions in CHG context: 3658 Total C to T conversions in CHH context: 5789 C methylated in CpG context: 1.2% C methylated in CHG context: 4.3% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104/CpG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104/CpG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 778 lines in total Total number of methylation call strings processed: 1556 Final Cytosine Methylation Report ================================= Total number of C's analysed: 25908 Total methylated C's in CpG context: 141 Total methylated C's in CHG context: 274 Total methylated C's in CHH context: 229 Total C to T conversions in CpG context: 7575 Total C to T conversions in CHG context: 7400 Total C to T conversions in CHH context: 10289 C methylated in CpG context: 1.8% C methylated in CHG context: 3.6% C methylated in CHH context: 2.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104/CpG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104/CpG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-168_S11_L002_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 545 lines in total Total number of methylation call strings processed: 1090 Final Cytosine Methylation Report ================================= Total number of C's analysed: 15205 Total methylated C's in CpG context: 50 Total methylated C's in CHG context: 157 Total methylated C's in CHH context: 81 Total C to T conversions in CpG context: 4307 Total C to T conversions in CHG context: 4240 Total C to T conversions in CHH context: 6370 C methylated in CpG context: 1.1% C methylated in CHG context: 3.6% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 99 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104/CpG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104/CpG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 306 lines in total Total number of methylation call strings processed: 612 Final Cytosine Methylation Report ================================= Total number of C's analysed: 7462 Total methylated C's in CpG context: 35 Total methylated C's in CHG context: 97 Total methylated C's in CHH context: 37 Total C to T conversions in CpG context: 2155 Total C to T conversions in CHG context: 1968 Total C to T conversions in CHH context: 3170 C methylated in CpG context: 1.6% C methylated in CHG context: 4.7% C methylated in CHH context: 1.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104/CpG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104/CpG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:J02459.1 LN:48502 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/lambda -p 4 -u 100000 -score_min L,0,-0.6 -1 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R1_001_val_1.fq.gz -2 /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-170_S13_L002_R2_001_val_2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 Processed 446 lines in total Total number of methylation call strings processed: 892 Final Cytosine Methylation Report ================================= Total number of C's analysed: 10292 Total methylated C's in CpG context: 33 Total methylated C's in CHG context: 134 Total methylated C's in CHH context: 51 Total C to T conversions in CpG context: 2966 Total C to T conversions in CHG context: 2731 Total C to T conversions in CHH context: 4377 C methylated in CpG context: 1.1% C methylated in CHG context: 4.7% C methylated in CHH context: 1.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 101 Maximum read length of Read 2: 98 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_CTOB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_CTOB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CHH_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CpG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt CHH_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/1104/CpG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/1104/CpG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Found 12 alignment reports in current directory. Now trying to figure out whether there are corresponding optional reports Writing Bismark HTML report to >> EPI-151_S2_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-151_S2_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-151_S2_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-152_S3_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-152_S3_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-152_S3_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-153_S4_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-153_S4_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-153_S4_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-154_S5_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-154_S5_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-154_S5_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-159_S6_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-159_S6_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-159_S6_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-160_S7_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-160_S7_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-160_S7_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-161_S8_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-161_S8_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-161_S8_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-162_S9_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-162_S9_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-162_S9_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-167_S10_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-167_S10_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-167_S10_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-168_S11_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-168_S11_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-168_S11_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-169_S12_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-169_S12_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-169_S12_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> EPI-170_S13_L002_R1_001_val_1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > EPI-170_S13_L002_R1_001_val_1_bismark_bt2_PE_report.txt < Processing alignment report EPI-170_S13_L002_R1_001_val_1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== No Bismark/Bowtie2 single-end BAM files detected Found Bismark/Bowtie2 paired-end files No Bismark/HISAT2 single-end BAM files detected No Bismark/HISAT2 paired-end BAM files detected Generating Bismark summary report from 12 Bismark BAM file(s)... >> Reading from Bismark report: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-160_S7_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_PE_report.txt >> Reading from Bismark report: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_PE_report.txt Wrote Bismark project summary to >> bismark_summary_report.html << [bam_sort_core] merging from 0 files and 28 in-memory blocks...